at OpenHelix

Antique (or maybe “classic”) UCSC Genome Browsers retired

Everyone is pretty comfortable with the concept of the non-standard but commonly used dog-years as a way to compare life spans to humans. Car enthusiasts have a taxonomy for the ages of vehicles. But I’ve been sitting here wondering what the genome-browser-years scale should be. I’ve been thinking about it because of the recent announcement over the UCSC list the other day:

Over the past 12 years we have made efforts to maintain visualization of many old, archived assemblies on our Archive server at http://genome-archive.cse.ucsc.edu/, in addition to providing download access to the associated data sets. Unfortunately, this visualization is no longer sustainable for very old assemblies due to the many changes in the Genome Browser software as it has matured. We are therefore reducing access to certain old assemblies to data downloads only, and are announcing the shutdown of our Archive server. We will continue to provide Genome Browser access for the 4 most current human assemblies, and at least the 2 most current assemblies for all other organisms with some exceptions. We will discontinue our visualization support for all other old assemblies, but will continue to make these data sets available on our download servers. The assemblies currently on our archive server for which we have discontinued visualization support include early human assembly drafts, hg4, hg5, hg6, hg7, hg8, hg10, hg11, hg12, hg13, hg15, rn1, rn2, mm1, mm2, mm3, mm4, mm5, rheMac1, bosTau1, ce1, danRer1, and danRer2. Links to the data and annotations associated with these assemblies have been added in the appropriate places on our Downloads page at http://hgdownload.soe.ucsc.edu/. Please contact us if you have difficulty locating a data set of interest.

Matthew Speir
UCSC Genome Bioinformatics Group

A view of the UCSC Genome Browser in the early days, ~2004.

I’m sure the browser versions aren’t used very much anymore, but it was something I needed to be aware of. In our workshops I mention that the older versions have been available from the “archives” navigation on the landing page, but that will be gone now. Occasionally there are old papers that reference a genomic span that you want to revisit–but that’s becoming less common for those really old assemblies at this point. The data will persist for downloading, but the browser visuals will be gone. But it made me want to go back and look through my old materials to see what the early browsers looked like (click on the image to embiggen). A lot of the foundational structure is the same, but if you look at one of these old assemblies you might be surprised. A lot fewer tracks, that’s for sure. In my shot, there are only a few species in the Conservation track (human, chimp, mouse, rat, chicken). We just didn’t have that much data available–not just across species, but other types of techniques and tools. Fewer tracks. Fewer functionality buttons.

This was almost as much fun as looking back at the old NCBI interfaces that I remember from way back. Those of you who have been in this rodeo for a while may remember those. Some of you will even remember the key “Pedro’s Tools” from back in the day. Sometimes it’s worth looking back at where we came from to realize how much further we are than we realized. I know there’s a lot of grousing about not having cured cancer and changed the pharmaceutical industry with the human genome sequence yet–but we really haven’t had the data that long in browser-years. Or maybe it’s more like Mars years–longer than you realize, despite the fairly comparable span of a single day. The arc of science is long, but it bends toward answers.

Edit: I realized I should look at the earliest paper and add that reference below. Check out Figure 1 for an even older view of the data.